tiling multiple chain structures
Hi chimera team, Sorry for pestering you again so soon! Very quick question though. If I have a couple of structures on screen which are made up of multiple PDBs, is there any way to tile them, but as groups? e.g. if I have one complex A-B-C, and another X-Y-Z, that I group into Group1 and Group2, I'd like to tile group1 and group2 next to each other. The tile command, as far as I can tell, is only capable of tiling A B C X Y Z as seperate models though (unless I went through the process of saving them all as a single PDB first). Is there any way to do this without the hassle of saving and reloading? Many thanks! Joe Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
Hi Joe, If there aren’t too many sets of models (say not more than 4-6) what I usually do to offset them for figures is not to use “tile” but instead: (1) superimpose or center all sets so they are in the desired rotational orientation. You can use the “S” checkboxes in the Model Panel to hide/show if it’s too much to view all at once. If they are all related structures, you could superimpose them, or at least their related subunits, with matchmaker. (2) simply use the “move” command to translate sets of models in X and Y until they are where you want them. E.g. to move models 4,6,7 horizontally to the left 20 angstroms, move x -20 models #4,6,7 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> (3) because of perspective, as you translate things away from center they may appear to be a in a slightly different orientation, so it may be useful to turn off perspective (command: set projection orthographic) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#projection> (4) saving positions is helpful in case you mess something up… i.e. after the first step above, use “savepos” so you could “reset” to that in the event of moving mistakes. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 19, 2018, at 6:46 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi chimera team, Sorry for pestering you again so soon!
Very quick question though. If I have a couple of structures on screen which are made up of multiple PDBs, is there any way to tile them, but as groups?
e.g. if I have one complex A-B-C, and another X-Y-Z, that I group into Group1 and Group2, I'd like to tile group1 and group2 next to each other.
The tile command, as far as I can tell, is only capable of tiling A B C X Y Z as seperate models though (unless I went through the process of saving them all as a single PDB first).
Is there any way to do this without the hassle of saving and reloading?
Many thanks! Joe
Hi Elaine/All, I thought I'd add to this thread again as I've figured out that the way to enable tiling of multiple chain structures is to first 'combine' them, which then treats them as a single model, rather than trying to 'group' them which seems to allow splitting of the models. Combined models are still able to have chains selected individually and manipulated as normal as far as I can tell. Hope this helps people in future! Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 19 April 2018 17:46:16 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] tiling multiple chain structures Hi Joe, If there aren’t too many sets of models (say not more than 4-6) what I usually do to offset them for figures is not to use “tile” but instead: (1) superimpose or center all sets so they are in the desired rotational orientation. You can use the “S” checkboxes in the Model Panel to hide/show if it’s too much to view all at once. If they are all related structures, you could superimpose them, or at least their related subunits, with matchmaker. (2) simply use the “move” command to translate sets of models in X and Y until they are where you want them. E.g. to move models 4,6,7 horizontally to the left 20 angstroms, move x -20 models #4,6,7 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> (3) because of perspective, as you translate things away from center they may appear to be a in a slightly different orientation, so it may be useful to turn off perspective (command: set projection orthographic) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#projection> (4) saving positions is helpful in case you mess something up… i.e. after the first step above, use “savepos” so you could “reset” to that in the event of moving mistakes. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 19, 2018, at 6:46 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi chimera team, Sorry for pestering you again so soon!
Very quick question though. If I have a couple of structures on screen which are made up of multiple PDBs, is there any way to tile them, but as groups?
e.g. if I have one complex A-B-C, and another X-Y-Z, that I group into Group1 and Group2, I'd like to tile group1 and group2 next to each other.
The tile command, as far as I can tell, is only capable of tiling A B C X Y Z as seperate models though (unless I went through the process of saving them all as a single PDB first).
Is there any way to do this without the hassle of saving and reloading?
Many thanks! Joe
participants (2)
-
Elaine Meng -
Healey, Joe